qpcR: Cy0 – R documentation

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Cy0

Cy0 alternative to threshold cycles as in Guescini et al. (2008)

Description

An alternative to the classical crossing point/threshold cycle estimation as described in Guescini et al (2002). A tangent is fit to the first derivative maximum (point of inflection) of the modeled curve and the intersection with the x-axis is calculated.

Usage

Cy0(object, plot = FALSE, add = FALSE, ...)

Arguments

`object`	a fitted object of class 'pcrfit'.
`plot`	if `TRUE`, displays a plot of Cy0.
`add`	if `TRUE`, a plot is added to any other existing plot, i.e. as from `plot.pcrfit`.
`...`	other parameters to be passed to `plot.pcrfit` or `points`.

Details

The function calculates the first derivative maximum (cpD1) of the curve and the slope and fluorescence F_{cpD2} at that point. Cy0 is then calculated by Cy_0 = cpD1 - \frac{F_{cpD2}}{slope}.

Value

The Cy_0 value.

Author(s)

Andrej-Nikolai Spiess

References

A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition.
Guescini M, Sisti D, Rocchi MB, Stocchi L & Stocchi V.
BMC Bioinformatics (2008), 9: 326.

Examples

## Single curve with plot.
m1 <- pcrfit(reps, 1, 2, l5)
Cy0(m1, plot = TRUE)

## Add to 'efficiency' plot.
efficiency(m1)
Cy0(m1, add = TRUE)

## Compare s.d. of replicates between
## Cy0 and cpD2 method. cpD2 wins!
ml1 <- modlist(reps, model = l4)
cy0 <- sapply(ml1, function(x) Cy0(x))
cpd2 <- sapply(ml1, function(x) efficiency(x, plot = FALSE)$cpD2)
tapply(cy0, gl(7, 4), function(x) sd(x))
tapply(cpd2, gl(7, 4), function(x) sd(x))

qpcR

Modelling and Analysis of Real-Time PCR Data

v1.4-1

GPL (>= 2)

Authors

Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>

Initial release

2018-05-29

Cy0